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10-11-2010, 09:20 PM
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#1 |
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Junior Member
Location: shanghai Join Date: Nov 2009
Posts: 8
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question about Solid data analysis using bowtie?
 hello ,everyone I am trying to run bowtie with the solid sequence data flower9_1_F3.csfasta and flower9_1_F3_QV.qual I built the bowtie-build -C index successfully and moved the generated index files to the Bowtie indexes subdirectory. I run the command: bowtie -n 3 --best --strata -a -e 150 -p 4 ../cDNA_reference/TAIR9_cdna -C -f flower9_1_F3.csfasta -Q flower9_1_F3_QV.qual --un fllower9-unmap > flower9-map & and the output i got is an error showing on console [wanglei@mu01 data]$ [wanglei@mu01 data]$ Too few quality values for read: 425_2031_2008_F3 are you sure this is a FASTQ-int file? terminate called after throwing an instance of 'int' Too few quality values for read: 425_2042_1847_F3 are you sure this is a FASTQ-int file? terminate called after throwing an instance of 'int' Too few quality values for read: 1277_2042_2013_F3 are you sure this is a FASTQ-int file? Could you please help me to sort out this issue? thanks wanglei |
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10-12-2010, 12:36 AM
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#2 |
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Nils Homer
Location: Boston, MA, USA Join Date: Nov 2008
Posts: 1,285
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Please only post to one forum. Cross-posting is like spam, unacceptable.
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10-12-2010, 03:38 AM
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#3 |
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Junior Member
Location: shanghai Join Date: Nov 2009
Posts: 8
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ok,i have deleted it, thanks!
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10-22-2010, 12:42 PM
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#4 |
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Member
Location: Iowa City, IA Join Date: Jul 2010
Posts: 95
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Truncated Qual file
I have had this error when SAET failed and a truncated qual file was produced.
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10-20-2012, 01:18 PM
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#5 |
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Member
Location: Norway Join Date: Nov 2011
Posts: 23
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Hey guys,
How did you solve this problem ? Could you please help me with this ? I am also getting this error, when using tophat mapping on colorspace file. This is my command: [Works fine until half-way] tophat --output-dir /results --color -p 8 --no-coverage-search /bowtie_alignment_reference/mm9_c F3.csfasta F3.QV.qual I get this error: Mapping left_kept_reads_seg1 to genome mm9_c with Bowtie (1/3) Mapping left_kept_reads_seg2 to genome mm9_c with Bowtie (2/3) Mapping left_kept_reads_seg3 to genome mm9_c with Bowtie (3/3) [2012-10-20 22:11:02] Mapping right_kept_reads to genome mm9_c with Bowtie [FAILED] Error running bowtie: Too few quality values for read: 39 I are you sure this is a FASTQ-int file? terminate called after throwing an instance of 'int' regards Chirag |
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03-26-2013, 07:32 AM
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#6 |
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Member
Location: The netherlands Join Date: Nov 2012
Posts: 38
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Did anyone of you solve this problem?
I have exactly the same problem now. Mapping left_kept_reads to genome GRCh37_gatk_colorspace with Bowtie Mapping left_kept_reads_seg1 to genome GRCh37_gatk_colorspace with Bowtie (1/2) Mapping left_kept_reads_seg2 to genome GRCh37_gatk_colorspace with Bowtie (2/2) Mapping right_kept_reads to genome GRCh37_gatk_colorspace with Bowtie [FAILED] Error running bowtie: Too few quality values for read: 28 I are you sure this is a FASTQ-int file? terminate called after throwing an instance of 'int' All 4 files are exactly 200000 lines (so 100000 reads). Mapping the left reads works, but when mapping the right reads it fails... [EDIT] For anyone who has this error too, check whether you have added the --quals option, also check the command on order of files (first all csfasta files than the qual files). This solved my error... Last edited by Jetse; 03-26-2013 at 09:02 AM. Reason: solved |
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